Index of values

Example: call "gunzip <list of fastq.gz files> > some_name_cat.fastq".

Create a fastq_reads workflow_node from one or two single_file workflow_node(s).

This functions guesses whether to use fastq or fastq_gz given the file name extension.

Transform a value of type Input.t into a pipeline returning FASTQ data, providing the necessary intermediary steps.

Run OptiType in `RNA or `DNA mode.

Create a kallisto specific index of the transcriptome (cDNA)

Used to determine if features in multiple sets intersect with one another.

Merge a list of BAM files.

Call somatic variants with Mutect2.

Quantify transcript abundance from RNA fastqs, results in abundance.tsv file

Run a program that does not use much memory, runs on one core, and needs the internet.

Run a program that does not use much memory and runs on one core.

Uses "samtools sort" if the input_bam is not tagged as “sorted as the ~by argument.” If it is indeed already sorted the function returns the input_bam node as is.

A stream processor, for this purpose, is a program that runs on one core and does not grow in memory arbitrarily.

Strelka is built from source but does not seem to build on MacOSX.

Make a filename-compliant string out of a region specification.

This is used to opacify the type of the expression.

Make a new bam sharing most of the metadata.

Concatenate VCFs using "vcftools concat".

Concatenate VCF files.

Call a command on a list of ~vcfs to produce a given ~final_vcf (hence the n-to-1 naming).

Sort a VCF file by choromosome position (it uses "vcf-sort" which itself relies on the "sort" unix tool having the "--version-sort" option).

Metadata generated at compile-time